AMBER Archive (2005)

Subject: AMBER: Sander minimization & dynamic question

From: chaiann ng (andy810915_at_hotmail.com)
Date: Mon Apr 04 2005 - 05:45:48 CDT

Dear Amber User:
 
I would like to hear some opinions from you guys about my method below.
 
I am doing modeling using NMR spectroscopy to obtain NOE constraints, and obtain intial structure from CYANA. What I want to achive is include the solvent in minimization and dynamic explicitly. My steps are:
1.  Min1, Min2, MD1, MD2 Running Minimisation and MD (in explicit solvent)(http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/section5.htm)
 
2. from MD2, I identify the 20 lowest energy structures from 500 structures (20ps-120ps) without the solvent present.
 
3. I redo the Min1 and Min2 with solvent at those 20 structures. That would be my final 20 structures for publication.
 
 
My questions and concerns are:
 
1. With explicit solvent, the dynamic can only be at room temperature. Am I correct?(http://amber.scripps.edu/tutorial/dna_NMR/nmr_dna_tutorial.htm)
 
2. Is there any problem with my method? Any suggestions?
 
 
 
 

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